A report on the 3rd International Legume Genetics and Genomics Conference, Brisbane,
Australia, 9-13 April 2006.

Meeting report

More than 230 delegates from 25 countries gathered in Australia recently for the latest
annual conference on legume genetics, where they heard an optimistic forecast for
the future of legumes as both an economic food commodity and a research topic, and
talks on topical subjects ranging from noncoding RNAs, signal transduction, stem-cell
research, and genomic profiling to pathogenic and symbiotic relationships. We have
selected a small number of highlights in these areas from the many talks that were
given at the meeting.

A valuable resource

Since the 1960s, the consumption of pulses has been going down, even in developing
countries, giving ground to meat and grains. Concurrently, interest in legume research
has waned and overall, plant-science graduates are scarce. But as Kofi Agblor (Saskatchewan
Pulse Growers Association, Saskatoon, Canada) reminded the meeting, remarkable parallels
exist between the recent economic history of mineral and energy resources and the
status of legumes. In the 20 years before 2001, mining became marginally profitable
and unfashionable, with declining investment in exploration, mines, and infrastructure.
Since the beginning of this century, however, mineral and energy commodity prices
have exploded. Today, everything in this field is at a premium, from geology graduates
to tyres for mining vehicles. Similarly, economic and social forces are gathering
that should again drive up legume cultivation and consumption, and give legume research
a higher profile.

As Agblor pointed out, several strands are coming together to make legumes more attractive:
protein security is precarious, as poultry, meat, and seafood are variously threatened
by bird flu, bovine spongiform encephalopathy (BSE), overfishing and heavy-metal contamination;
rates of diabetes and obesity are sky-rocketing in developed countries as a result
of diets containing too much fat and carbohydrate; and higher energy prices are increasing
the cost of nitrogen fertilizers. The high protein and oil content of pulses and the
ability to store protein easily in this form, combined with the ability of legumes
to provide their own nitrogen, is set to make legumes attractive crops again. They
may even have a future as a biofuel.

Nancy Terryn (Ghent University, Ghent, Belgium) reminded us, however, that there are
barriers to exploiting the full potential of legumes, especially in developing countries.
She argued that although low-level cultivation farming practices are environmentally
friendly, the resulting poor yields may be unacceptable when it comes to feeding growing
populations, as low-level cultivation requires up to three times the land area to
produce the same crop biomass compared to conventional farming practices. And potential
new crop legumes suitable for developing countries are not domesticated or improved
for agricultural use.

RNA regulators

John Mattick (University of Queensland, Brisbane, Australia) presented evidence that
multicellular organisms, including vascular plants, express a large repertoire of
non-coding RNAs, and that their likely role is to regulate and direct the complex
pathways of development in multicellular organisms. The function of some noncoding
RNAs is gene silencing, and Bernie Carroll, also from the University of Queensland,
reported elegant grafting experiments with Arabidopsis that showed the movement of RNA silencing from roots to shoots and identified several
genes required for the translocation of RNA silencing. In this context, Penny Smith
(University of Western Australia, Crawly, Australia) showed that microRNAs (miRNAs)
are prevalent in lupin phloem sap and that they may act as long-distance signal molecules.
Florian Fruiger (CNRS, Gif-sur-Yvette, France) described the use of overexpression
strategies that identified miRNAs that perturb root architecture in Medicago. Ralf Dietzgen (University of Queensland) described his group's work showing how
durable virus resistance mediated by RNA interference (RNAi) can be achieved by targeting
viral suppressors of RNA silencing and by simultaneously introducing target sequences
from different viruses. Jiayu Wen (Australian National University, Canberra, Australia)
showed that her in silico approach could identify over 2,000 non-coding RNA genes in Medicago truncatula and Lotus japonicum.

Dissecting pathways and gene families

One feature that makes legumes attractive as crops is their ability to fix atmospheric
nitrogen by means of symbiotic bacteria - rhizobia and relatives - that live in nodules
in the legume's roots. During root-nodule formation, rhizobia secrete lipochitooligosaccharide
molecules called Nod factors; these recognize plant serine/threonine receptor kinases
(NFR1 and NFR5) with LysM domains, and induce a series of downstream responses, initially
in root hair cells, that lead to the expression of plant nodulation genes. Simona
Radutoiu (University of Aarhus, Denmark) reported domain-swapping experiments that
demonstrated the involvement of the receptor's LysM domains in the perception of Nod
factors. Giles Oldroyd (John Innes Centre, Norwich, UK) described elegant work by
his group showing that a gain-of-function mutation in the plant chimeric calcium/calmodulin-dependent
protein kinase DMI3 activates the expression of plant nodulation genes independent
of Nod factors. They showed that the gain of function requires the actions of two
GRAS-family transcriptional regulators, NSP1 and NSP2. By the use of NSP2-GFP fusions,
NSP2 was shown to relocate from the nuclear envelope/endoplasmic reticulum to the
nucleus upon Nod factor elicitation. They found that DMI3 kinase activity was activated
through the binding of calmodulin and calcium, and active DMI3 in turn regulated NSP2
activity to coordinate Nod-factor-induced gene expression. This indicates that NSP2
transduces calcium signals in plants.

The role of flavonoids in nodule initiation was explored by Gary Stacey (University
of Missouri, Columbia, USA) and Ulrike Mathesius (Australian National University,
Canberra, Australia), who both reported RNAi constructs, in soybeans and Medicago, respectively, that knocked down flavonoid pathway expression and abolished nodule
initiation. Flavonoid complementation of the nodulation aberration was possible with
Medicago but not with soybean, suggesting that there might be different flavonoid uptake systems,
a situation similar to that reported by one of us (C.B.) for Arabidopsis. Evidence for a role for flavonoids in affecting auxin levels was presented by Mathesius,
while Stacey concluded that abolishing induction of the Bradyrhizobium nod gene in the root environment caused nodulation failure rather than flavonoids
having a direct role in nodulation. In addition, Stacey described clever ways to visualize
extracellular ATP, by using a luciferase as a reporter, and to discern its role in
root-hair infection.

The control of petal shape and floral zygomorphy (bilateral symmetry) in Lotus was addressed by Da Luo (Shanghai Institute for Biological Sciences, Shanghai, China).
He reported work by his group showing that a member of the TCP-box gene family, CYC2 - whose function is mediated through an interaction with specific MYB genes - has
a 'dorsalizing' activity in petal development (that is changing all the petals to
that of dorsal petal identity). CYC2 may interact with the gene Kew1, which controls lateral petal formation, as CYC2 × Kew1 mutants only have ventral petal identities.

Steven Clark (University of Michigan, Ann Arbor, USA) described studies into how stem-cell
populations are maintained in the apical meristem, the growing point of a plant shoot.
These focused on teasing apart the contributions of individual members of the CLAVATA1
(CLV1), CLAVATA3 (CLV3), POLTERGEIST and REVOLUTA gene families in Arabidopsis. A key result was the characterization of the ability of different proteins containing
CLV3/ESR domains (CLEs) to replace the secreted peptide, CLV3, function in vivo. The team showed that the different CLEs each possess a signal peptide, a variable
domain and a conserved carboxy-terminal motif of approximately 15 amino acids, and
that CLE functions are likely to be determined by their conserved carboxy-terminal
domains. The next task will be to determine how active CLE peptides are cleaved from
the variable domain, and which protease carries out this task.

Strategies for invasion

Soil nematodes invade legume roots and new insights into legume-nematode interactions
were presented by David Bird (North Carolina State University, Raleigh, USA). Root-knot
nematodes (RKNs) were found to induce cytoskeletal responses in legume root hairs
similar to those elicited by Rhizobium Nod factors. Plants mutated in the Nod-factor receptors, Nfr1 and Nfr5, responded
only very weakly to RKNs, suggesting that RKNs produce a Nod factor-like compound(s).
In another case of molecular mimicry, soybean cyst nematodes were reported by Melissa
Goellner Mitchum (University of Missouri, Columbia, USA) to contain CLV3-like elements
in their genomes that may play a role in infection by aiding a successful interaction
that does not trigger a defence response.

Karam Singh (CSIRO, Wembly, Australia) presented work on the genetic resistance to
bluegreen aphid or blue alfalfa aphid identified in M. truncatula and backcrossed into susceptible cultivars. The presence of the resistance gene makes
the resistant plant less attractive to aphid infestation. The resistance segregates
as a single dominant gene, AKR. Helge Küster (Centre for Biotechnology, Bielefeld, Germany) has used 70-mer oligonucleotide
microarrays of Medicago to examine differential gene expression during nodulation and the formation of root
mycorrhiza, and has identified genes of interest including signal transduction and
transcription regulators many of which were not previously known. Prem Bhalla (University
of Melbourne, Parkvile, Australia) used RNA from microdissected shoot apical meristems
(SAMs) to probe microarrays and identify shoot apical meristem specific genes. To
address possible under-representation of SAM transcripts on microarrays, SAM cDNA
libraries were examined and more SAM-specific transcripts were identified. These included
LRR-kinase-like kinases, four integrin-like kinases, auxin binding proteins and auxin
efflux transporters.

It will be interesting to see the progress made by the next meeting in Mexico in 2008
and to find out whether legumes have indeed enjoyed the same renaissance as resource
commodities are undergoing now.